Table of Contents

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2019-10-14
   Biologics: Assay Management
     Biologics Assay Data
     Biologics: Upload Assay Data

Biologics: Assay Management


These topics explain how to set up and import assay data in LabKey Biologics:

Topics for Users

Topics for Administrators




Biologics Assay Data


Assay Data Dashboards

LabKey Biologics offers a number of different views on assay data in the system.

The main page of the Assays tab shows a heat map, with the available assays types as rows and the last twelve months as columns. Color density indicates the amount of assay data that has been entered into the system.

Clicking a cell in the heat map navigates to the data for the given assay type and month.

Each assay type has four tabs, showing various scopes of the data:

  • Overview - Displays the name and description for the assay.
  • Batches - Displays batch-level metadata about the assay results. Batches are the widest grouping of the data, presenting the broadest view of the data. Each batch generally groups together multiple runs (or files) of data.
  • Runs - Displays run-level metadata about the assay results. Runs are the mid-level grouping of the data, standing between the batches and the result data. Each run generally represents one file of data.
  • Results - Displays the result data of the assay, showing the data output of the instrument.

On assay data grids, any visualizations that have been added to the assay, can be seen by clicking the Charts button. If the Charts button is grey-out, then no visualizations have been associated with the current assay. (Administrators can add charts to an assay, as detailed in the topic: Biologics Admin: Charts and Custom Grids.)

Custom grid views are available by clicking the Grid Views button. (Administrators can add custom data grids to an assay, as detailed in the topic: Biologics Admin: Charts and Custom Grids.)

Assay Quality Control

Visibility of assay data in Biologics can be controlled by setting quality control states. To configure the available QC states in the system, administrators should see the following topic: Assay QC States - Admin Guide.

Once QC states have been configured in the system, users (with the appropriate roles) can assign those states to assay run data. Users can update QC states in the following cases:

  • when a user has both Reader and QC Analyst roles
    • OR
  • when a user has either Folder, Project, or Site Admin roles
To assign QC states:

  • Navigate to the assay run view page. (Cell Viability runs are shown below.)
  • Select one or more runs.
  • Select Manage Runs > Update QC States. (Admins will see Manage Runs > Update QC States, while QC Analysts will see only the Update QC States button.)
  • In the popup dialog, use the dropdown menu to select the QC state. This state will be applied to all of the runs selected.
  • Optionally add a comment.
  • Click Save changes.
  • The QC states will be reflected in the runs data grid. Admins and QC Analysts will see all of the runs, as shown below.
  • Readers may see a restricted view of the runs, if some of the QC states are not "Public Data". In this case a message will appear over the grid, as shown below.

Related Topics




Biologics: Upload Assay Data


Import Assay Data

To import new assay data:

  • Hover over Assays and select the assay design you wish to import into.
  • Select either Runs or Batches and click Import Data.
  • On the Data Import page fill out the form:
    • Batch Properties - (Optional) If the system has been configured to accept batch level properties, enter information to describe the batch.
    • Run Properties - (Optional) These properties capture the characteristics of this assay experiment, such as a unique id, the instrument settings, special circumstances, or which request this data fulfills.
      • Assay Id - If no id is supplied, then the assay file name will be used. If no file name is used, then an id will be created from the assay design name plus a time stamp.
      • Comments - Add text to record special circumstances connected to this assay run.
      • Assay Request - Select the original assay request, if any.
    • Run Data - There are three tabs in the Run Data panel. To help your data conform to the assay design, Download Template to use.
      • Upload Files - On this tab (shown in the screencap above), you can either click the (paperclip) icon to browse to your assay data file or you can drag and drop the file onto the upload area.
      • Copy-and-paste Data - On this tab, you can copy-and-paste your data into a text box.
      • Enter Data Into Grid - On this tab, you can manually enter data (at the run level only).
  • Click Save and Finish or Save and Import Another Run.

Import Assay Data Associated with a Sample

An alternative way to import assay data lets you directly associate assay data with some sample(s) in the registry.

From the Samples grid, select one or more samples, and then select Insert New > Upload Assay Data. The menu will expand to show the assay options from which to select.

The assay import form will be pre-populated with the selected samples, as shown below. (Note that only manual data entry is supported for this style of entering assay data.)

Re-Import Run

In cases where you need to revise assay data after uploading to the server, you can replace the data by "re-importing" a run.

To re-import a run of assay data:

  • Go the details page for the target run. (For example, go to the runs table for an assay, and click one of the runs.)
  • Click the triple bar icon () and select Re-import Run.
  • Re-enter any batch and run properties, and select the new assay data file to replace the data currently on the server.
  • Click Save and Finish.
  • The data replacement event is recorded by the "Replaced By" field.

Delete Assay Run

To delete an assay run:

  • Go the details page for the target run. (For example, go to the runs table for an assay, and click one of the runs.)
  • Click the triple bar icon () and select Delete Run.
  • On the Confirm Deletion page, click Confirm Delete.